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- PDB-7y9a: Crystal structure of sDscam Ig1-2 domains, isoform beta2v6 -

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Basic information

Entry
Database: PDB / ID: 7y9a
TitleCrystal structure of sDscam Ig1-2 domains, isoform beta2v6
ComponentsDown Syndrome Cell Adhesion Molecules
KeywordsCELL ADHESION / cell surface receptor
Biological speciesChelicerata (chelicerates)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChen, Q. / Yu, Y. / Cheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for the self-recognition of sDSCAM in Chelicerata.
Authors: Cheng, J. / Yu, Y. / Wang, X. / Zheng, X. / Liu, T. / Hu, D. / Jin, Y. / Lai, Y. / Fu, T.M. / Chen, Q.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Down Syndrome Cell Adhesion Molecules
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0893
Polymers21,3311
Non-polymers1,7582
Water27015
1
A: Down Syndrome Cell Adhesion Molecules
hetero molecules

A: Down Syndrome Cell Adhesion Molecules
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1776
Polymers42,6622
Non-polymers3,5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5760 Å2
ΔGint59 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.256, 49.018, 82.024
Angle α, β, γ (deg.)90.000, 104.663, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein Down Syndrome Cell Adhesion Molecules


Mass: 21331.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Trichoplusia ni (cabbage looper)
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-3][LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH7.0, 20 % (w/v) PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8315 / % possible obs: 98.8 % / Redundancy: 6 % / Biso Wilson estimate: 46 Å2 / CC1/2: 0.971 / CC star: 0.993 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.038 / Rrim(I) all: 0.095 / Χ2: 1.477 / Net I/σ(I): 9.1 / Num. measured all: 50140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.10.2113740.9730.9930.0990.2340.95389.7
2.54-2.5950.223920.9670.9920.1040.2440.9395.1
2.59-2.645.20.1994110.9690.9920.0950.2221.00996.9
2.64-2.695.30.1824040.9810.9950.0840.2011.23296
2.69-2.755.30.1734020.9870.9970.0810.1921.16599.5
2.75-2.825.30.1664220.9880.9970.0760.1831.16399.8
2.82-2.8960.1664080.9730.9930.0760.1831.108100
2.89-2.966.30.1484230.9920.9980.0630.1621.214100
2.96-3.056.30.1444120.9910.9980.0630.1581.223100
3.05-3.156.50.1214200.9940.9980.0520.1321.331100
3.15-3.266.40.1114130.9940.9990.0480.1211.232100
3.26-3.396.10.114280.9880.9970.0490.121.525100
3.39-3.556.20.1054120.990.9970.0460.1151.677100
3.55-3.736.80.0934250.9960.9990.0390.1011.583100
3.73-3.976.60.0864230.9940.9980.0360.0941.736100
3.97-4.276.60.0754210.9960.9990.0320.0811.816100
4.27-4.76.20.0734220.9930.9980.0330.0811.853100
4.7-5.386.80.0714240.9950.9990.0290.0771.788100
5.38-6.786.20.0694310.9950.9990.030.0761.684100
6.78-506.10.0684480.9960.9990.0290.0752.58999.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DMK

3dmk


Resolution: 2.51→26.88 Å / SU ML: 0.4202 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 32.9393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2785 418 5.05 %
Rwork0.2413 7867 -
obs0.2432 8285 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.73 Å2
Refinement stepCycle: LAST / Resolution: 2.51→26.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 118 15 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631627
X-RAY DIFFRACTIONf_angle_d1.08122227
X-RAY DIFFRACTIONf_chiral_restr0.0746294
X-RAY DIFFRACTIONf_plane_restr0.0052263
X-RAY DIFFRACTIONf_dihedral_angle_d4.4936974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.870.35921280.30732506X-RAY DIFFRACTION94.14
2.87-3.620.32791430.26532649X-RAY DIFFRACTION99.89
3.62-26.880.23671470.21412712X-RAY DIFFRACTION99.51

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